Continuity mistake: When Prince Nuada holds up the golden egg-shaped "Forest God" pod, it's in his right hand. After it opens and he goes to take out the green object, he's holding it in his left hand and takes it out with his right hand.
Continuity mistake: When Prince Nuada defies his father, he kills every royal guardsman in a matter of seconds. There are only two guards left, and he kills them, also, before he kills his father. As Nuada kills his father, we see Mr. Wink in the background, fighting a very-much-alive royal guardsman.
Continuity mistake: When Abe and Hellboy get drunk together, they move into the bedroom where Liz is sleeping. To start off with Hellboy is to the right of Abe and Abe is to the left of Hellboy, but suddenly we get a different view and this time it's a mirror image - Hellboy is to the left of Abe and Abe is to the right of Hellboy.